Stargate Atlantis: Phantoms of Pegasus
by Delta105
Summary: A plan to ambush two Wraith Hive ships goes south on the crew of the Earth ship, Sentinel. The ship disappears. The Atlantis team must find out what happened to the ship and what the Wraith plan to do with it's wealth of technology. Please review!
1. Prologue

Colonel Reynolds stared out of the main view port of the Sentinel, the ship under his command. Arms crossed and eyebrows furrowed, he thought about why he was out here. In the farthest reaches of his world. In the Pegasus galaxy.

He was under orders from General Landry, head of Stargate Command, to scout out known Wraith hive locations to determine the threat to Earth and its allies back in the Milky Way galaxy.

His ship, the Sentinel, was a 304 class Battle Cruiser. Sister ship to all the other 304's. One of which was recently finished, called the Pandora. The Pandora was back home in the Milky Way doing hit and run missions against Lucian Alliance cargo ships.

The Colonels mind wandered toward the mission reports he had read on the Wraith. Of how they had terrorized the people of the Pegasus galaxy for thousands of years. Of how they never died of old age. Of how they had ships the size of large cites. And of course, of how they fed by literally sucking the life out of you through your chest.

Reynolds shivered. The feeding process was excruciatingly painful; he had known people who were killed by the Wraith. It was just evil, how the Wraith had terrorized civilizations in Pegasus for that long. Any world that tried to fight was exterminated like a pesky group of insects.

The Lieutenant overlooking the navigations console said something and jerked him out of his thoughts.

"Sir? We're about to reach our destination."

"Ok, drop us out."

The view in the window went from the blurry blue haze of hyperspace back into the black curtain of normal space.

"According to our Intel, the Wraith hives should be gathering around the far side of that planet." He pointed to the large red sphere to the right of their view. "M1M-837. Bring us around and stop just outside of sensor range, then I want the two Jumpers to get out there and do some scouting on those Hive ships."

Six minutes later the Sentinel was in position and the small Jumper fighters were being launched out of the fighter bays. He watched the tube-like ships fly away before they disappeared with their renowned cloak mode. The Colonel knew it would take at least 15 minutes before the tiny cloaked fighters were in position and ready to relay information back to them, so he decided to sit in his command chair for now.

The bridge was silent for the entire time. 13 minutes later the voice of the pilot in Jumper 1 sounded in his earpiece.

"_Bad news, sir."_

"I thought I told you to maintain radio silence?"

"_Sir, I know, but the Intel was a bust. We've scanned for Hive ships but there's nothing out here."_

"Scan again."

"_We did."_

The Colonel closed his eyes and shook his head in annoyance. They had flown to Pegasus from Milky Way as fast as they could, pushing engines at 120% so they could find the Wraith days before they even left the area. The entire trip took 2 weeks. Now they had to turn around and head back with empty pockets.

"Tell Jumpers 1 and 2 to head back, we're going home."

"Sir? They could show up late."

"The Wraith were supposed to be here in the first place. We're not waiting around for something that won't show up."

Just then short range sensors console emitted an alarm. Out the main view port the Colonel watched as a hyper space window opened right above their heads. Out of it emerged a wraith Hive ship.

"A Hive ship just arrived. They're powering weapons!"

"All batteries open fire. Evasive maneuvers until we can pick up those jumpers."

He watched as yellow rail gun rounds streaked toward their target. The missiles soon followed.

"They're launching Darts!"

The fighters, called "Darts" because of their pointed look, fired on the Sentinel as they left the Hive's fighter bays. The Dart fire combined with bombardment from the Hive pounded hard on their shields.

"Shields down to 60%!"

"We can't pick up the jumpers. Tell them to head down to the Stargate on the planet, and get clear of that hive ship. Arm our nuclear warhead, let's hope they haven't jammed us yet."

The Hive ship and Darts continued to pound on the Sentinel.

"Shields at 20%!"

The Colonel glared out at the Hive ship.

"Shields are depleted!"

Reynolds chair shook as his ships armor plating started taking the hits.

"Warhead is armed. Detonation set 1 second after departure."

"Beam it."

"The radiation will hit us."

"We can't outrun the Hive, and there's too many Darts to risk a jump out of here, this is our last chance. Beam it."

The main view port filled up with a bright blue light. Colonel Reynolds looked away before it blinded him.

Once the light cleared, he looked at where the Hive used to be. Nothing remained.

The radiation hit them a few seconds after the blast. Almost all primary systems and most secondary systems on the ship started to shut down. Weapons control, engines, even sub-space communications all went down. They were dead in the water.

"Damage report."

"Shields are down completely. Two of the lower decks are venting atmosphere, and severe damage to the hull on the nose of the ship. All weapons are down except for rail guns. We can't use the beaming technology either."

"Seal off all damaged sections. I want our engines back up so we can get out of here. What about the radiation?"

"At this distance it's not lethal, we should be fine."

"Sir! Four more Wraith ships just jumped in. Two cruisers and two Hives."

"God damn it. Open fire and scramble the F-302's!"

Remaining rail guns opened up on the Hive ships as the F-302's left the Sentinel. Reynolds knew they wouldn't be coming back.

"Get those fucking engines going now!" the Colonel ordered.

"The engineers say they can't get them working in time!"

The Hives targeted their rail guns, but left the integrity of the ship itself alone.

"Sir! We're being boarded!"

The Hives ceased fire on the Sentinel, boarding parties of Wraith marched into the BC-304 via the fighter bays.

"Orders sir?"

"Get to the nearest armory and arm yourselves."

Just then the Colonel realized that the Wraith had planned this all along. They had purposely sacrificed one of their ships to bring down their shields and used the radiation from the nuke to fry the Sentinels systems. He had to give them credit, they were ambitious little bastards.

He started to hear the stunner blasts from Wraith weapons down the stairwell next to him.

Without the beaming technology working they couldn't escape to the nearby planet. Help wasn't coming and the Wraith outnumbered them 50 to 1. They grabbed some weapons and cover. The Colonel and his crew waited for their last stand against the Wraith.


	2. Chapter 1

Colonel Sheppard stepped over the fallen tree, quietly sneaking over the crunchy dry leaves that scattered the forest ground. They were in hostile territory, the Wraith were at this world a few days ago. They could still reside, camouflaged, among the trees. Telya and Ronon flanked either side of him, with Dr. McKay shuffling loudly behind them. The doctor was, as usual, focusing on the life signs detector in his hand. Sheppard knew this device had is uses, but the naked eye is always true.

Ronon held his fist up, signaling the group to stop. They all crouched down, save for McKay, who took a few seconds before he realized what was going on. Ronon pointed to their 10 o'clock. Sheppard to could see something round through the trees. They advanced slowly, watching for hostiles all around as they got closer.

Sheppard looked at the cylinder through the trees. It was a jumper, half embedded cockpit first into the ground on a slant.

"Could be a trap." Ronan whispered.

"Everything's a trap with you, Ackbar." Sheppard remarked.

"What did you call me?"

"Never mind, let's check it out."

"This is Jumper #13, assigned to the Sentinel a few weeks ago." McKay stated.

"How'd it get on the planet then? They were supposed to stay in space." Sheppard asked.

"Oh I'm sorry, how silly of me to not know by now, lemme check the Captains log, what Stardate is it?"

"Very funny."

"Give me a few minutes to unscramble the bypass codes. Then I can get into the Jumpers memory core."

"Okay, just hurry up, a Wraith battalion could show up at any moment."

"Oh thanks, like I needed to be reminded we're on a hostile planet. Not to mention the fact that this planet is extremely dry, and it's gonna cause my skin to get rashes if we stay out here much longer. Plus there's all these mosquito things flying around. What if one bites me and I'm allergic? Like I am with citrus? Hey that plant right there doesn't have any lemon or orange looking things on it, right? Because I'm-"

"McKay!"

"Oh, right…"

McKay went over to the jumper an climbed in the rear hatch.

"So McKay's probably gonna be quite a few minutes. Teyla, you come with me, Ronon, stay with McKay. We're gonna have a look around. See if the passengers are close by." Said Sheppard.

"I do not believe the Wraith would give up on the chase. The passengers are probably dead or taken aboard a Hive ship." Stated Teyla.

"Well we don't leave our people behind. We won't give up on them. Let's go," He looks at Ronon, "Make sure McKay doesn't get sidetracked."

Shepard and Teyla walked through a thick bramble of bushes searching for any sign of the missing crew of the crashed jumper. The dense trees would have obscured their view from above, so they came through the 'gate on foot.

The trees started to thin out , before long they wandered into a large clearing.

"Sheppard, look at this." Teyla called him over.

Sheppard walked over to where Teyla was standing, observing something on the ground.

"Footprints."

"Yes, that is what it appears to be."

"Looks like one of our people."

"It seems like that to me as well."

Sheppard started following were the footprints led, he noticed there was another pair beside them. They led away from the jumper crash site.

"I think they were trying to put as much distance between them and the jumper as they could. They're going in a straight line away from it," stated Sheppard.

"Perhaps to escape the Wraith?"

"If they were involved, which I would bet my only copy of 'War and Peace' they were."

"Ugh, looks like the crew was messing around with all these control panels before they left." Mckay said.

"Hey."

"What?" Mckay snapped.

"Any guesses on what shot this thing down?" Ronon asked.

"Well judging from the specific radiation levels coming from the holes on the side that could have only been caused by Wraith weapons, I'd say…oh let's see…perhaps Wraith?"

"You could've just said 'Wraith'."

"Well it's not nearly quite as satisfying." Mckay said as he pried open a fried, blackened control console. "Ah, here we go."

"What is it?"

"The memory core, now it's just hack, then plug 'n' play from here."

Sheppard continued to follow the tracks, walking at a quickened pace.

"Ronon this is Sheppard, I found the tracks of what is most likely the crew of the crashed jumper. I'm following it now"

"Alright, and Mckay's found the-"

"I've found the memory core, I'm attempting to get the bypass codes so I can see what happened to the jumper." Mckay interrupted.

"That's good news, I'll check back in once I've found something, Sheppard out."

Sheppard continued to follow the tracks, they were nearing the middle of the clearing now. Teyla was also watching the prints as they disappeared under their steps. Then she noticed something.

"It appears as if they started running." She observed.

"Yeah, their prints are spaced farther and they look more dug into the ground."

They kept following the suspenseful trail.

"They're running full tilt now." Sheppard said.

"Running for their lives?"

"Maybe."

Then the tracks suddenly stopped. Not as in they started walking again, no, the tracks simply disappeared. Cut off. Ended. There was nothing left to follow.

"They were culled."

Sheppard and Teyla turned and ran back towards the jumper."

Mckay carefully lifted the memory core out from inside the control panel. It was then realized why the jumpers controls looked like they had been played with since the crew left.

"Oh no. Oh no, no, no." He said.

"What now?" Ronon complained.

Mckay didn't respond, he just held up a small device in his hand. Ronon recognized it as a sub-space tracking device. The Wraith used it to broadcast a beacon from across the galaxy. It was blinking and activated.

"Sheppard this is Mckay, we have a little problem here."

Sheppard slowed down to talk.

"What happened?"

"The jumper was a trap, taking out the memory activated a subspace tracking beacon."

"Alright take the memory core and head to the gate right now, don't stop for anything, Sheppard out." He looked at Teyla. "Come on, we'll meet them there."

Mckay and Ronon arrived at the 'gate first. Mckay started the dialing sequence back to Atlantis. The symbols on the DHD were burned into his memory after so much travel to and from Atlantis in the years he's been here. It was routine.

The fifth chevron was locking when the dialing sequence stopped, and then chevrons all glowed bright blue. Someone was dialing in.

"Sheppard," he yelled over the swoosh of the event horizon shooting out of the now-active stargate before it stabilized into a wormhole. "We've got 'gate activity!"

Three small ships shot out of the 'gate and raced off to the jumper crash site.

"Three darts just came through and are heading towards the jumper!"

"Alright, we'll watch our backs."

"It's your fronts you should be worried about since that's where they're coming from."

Sheppard and Teyla hit the deck as the darts passed over, searching in a "V" formation for whoever activated the beacon which was still in the Jumper. The darts must've missed them, for they passed over and didn't turn back. They waited a few seconds after the darts were out of sight before they got back up and ran for the direction of the 'gate.

Mckay and Ronon were waiting for them near the gate.

"Alright, let's get the hell outta here before they come back." Sheppard suggested.

They noticed a high pitched whining sound that was growing louder.

"Shit, here they come!"

McKay started the dialing sequence, fumbling in nervousness and almost dialing it wrong.

They could see the darts on the horizon as they opened fire on the small group. Wraith blasts hit the ground around them, throwing fire and dirt everywhere.

"Run for the 'gate!" Shepperd yelled over the dart blasts.

The 7th chevron locked and the wormhole swooshed into place once again.

"Atlantis, this is McKay, we're coming in hot!"

The Wraith darts were right on top of them. Ronin and Mckay made it to the gate first, Ronin ran through, but a dart blast hit the ground behind Mckay, launching him through the gate.

Sheppard watched in horror for his friend, and sprinted even harder for the 'gate, Teyla running at his heels. He could hear the sound of a culling beam behind him and dived for the gate, he hit the event horizon.

A cold floor rushed to meet him as he came through the other side of the 'gate. Teyla grunted as she hit the floor behind him. The wormhole collapsed and someone called for a medical team. He rolled over and one of the 'gate guards helped him to his feet. Sheppard looked around and saw McKay being lifted onto a stretcher. Mckay's backpack lay on the ground, smoking, probably what saved his life. Once again, they barely escape.


End file.
